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- EMDB-10102: Type III-B Cmr-beta Cryo-EM structure of the Apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-10102
TitleType III-B Cmr-beta Cryo-EM structure of the Apo state
Map data
Sample
  • Complex: Type III-B Cmr-beta binary complex, crRNA-bound
    • Protein or peptide: CRISPR-associated protein, Cmr5 family
    • Protein or peptide: CRISPR-associated RAMP protein, Cmr4 family
    • Protein or peptide: CRISPR-associated protein, Cmr3 family
    • Protein or peptide: CRISPR-associated RAMP protein, Cmr6 family
    • Protein or peptide: Cmr1
    • Protein or peptide: CRISPR-associated protein, Cmr2 family
    • RNA: crRNA (51-mer)
    • Protein or peptide: CRISPR-associated protein Cmrx
  • Ligand: ZINC ION
Function / homology
Function and homology information


CRISPR-cas system / defense response to virus / membrane / cytoplasm
Similarity search - Function
CRISPR system CMR subunit Cmr7 1 / CRISPR system CMR subunit Cmr7 1 / : / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein TM1795 / CRISPR-associated protein, Cmr3 / : / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 ...CRISPR system CMR subunit Cmr7 1 / CRISPR system CMR subunit Cmr7 1 / : / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein TM1795 / CRISPR-associated protein, Cmr3 / : / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / Cas10/Cmr2, second palm domain / CRISPR type III-associated protein / RAMP superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR-associated protein, Cmr3 family / CRISPR-associated protein, Cmr2 family / CRISPR-associated RAMP protein, Cmr6 family / CRISPR-associated RAMP protein, Cmr1 family / CRISPR type III-B/RAMP module-associated protein Cmr5 / CRISPR-associated RAMP protein, Cmr4 family / CRISPR-associated protein Cmrx
Similarity search - Component
Biological speciesSulfolobus islandicus REY15A (acidophilic) / Sulfolobus islandicus (strain REY15A) (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSofos N / Montoya G
Funding support Denmark, 3 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
Novo Nordisk FoundationNNF0024386 Denmark
Citation
Journal: Mol Cell / Year: 2020
Title: Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas.
Authors: Nicholas Sofos / Mingxia Feng / Stefano Stella / Tillmann Pape / Anders Fuglsang / Jinzhong Lin / Qihong Huang / Yingjun Li / Qunxin She / Guillermo Montoya /
Abstract: Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) ...Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific single-stranded RNA (ssRNA) hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-β, unveiling how binding of the target RNA regulates the Cmr2 activities. Cryoelectron microscopy (cryo-EM) analysis revealed the unique subunit architecture of Cmr-β and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA-bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5' tag in the CRISPR RNAs (crRNA) and the 3' antitag of the target RNA activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self- versus non-self-recognition. These findings highlight the diverse defense strategies of type III complexes.
#1: Journal: Biorxiv / Year: 2020
Title: Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas
Authors: Sofos N / Feng M / Stella S / Pape T / Fuglsang A / Lin J / Huang Q / Li Y / She Q / Montoya G
History
DepositionJul 2, 2019-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6s6b
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10102.png

Downloads & links

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Map

FileDownload / File: emd_10102.map.gz / Format: CCP4 / Size: 41 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 416. Å		0.83 Å/pix.
x 500 pix.
= 416. Å		0.83 Å/pix.
x 500 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-11.327906 - 23.335686
Average (Standard dev.)0.0035287677 (±0.60918933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA: 416.00003 Å / B: 415.99997 Å / C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-11.32823.3360.004

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Supplemental data

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Additional map: Model-sharpened and boxed out map

Fileemd_10102_additional.map
AnnotationModel-sharpened and boxed out map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10102_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10102_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type III-B Cmr-beta binary complex, crRNA-bound

EntireName: Type III-B Cmr-beta binary complex, crRNA-bound
Components
  • Complex: Type III-B Cmr-beta binary complex, crRNA-bound
    • Protein or peptide: CRISPR-associated protein, Cmr5 family
    • Protein or peptide: CRISPR-associated RAMP protein, Cmr4 family
    • Protein or peptide: CRISPR-associated protein, Cmr3 family
    • Protein or peptide: CRISPR-associated RAMP protein, Cmr6 family
    • Protein or peptide: Cmr1
    • Protein or peptide: CRISPR-associated protein, Cmr2 family
    • RNA: crRNA (51-mer)
    • Protein or peptide: CRISPR-associated protein Cmrx
  • Ligand: ZINC ION

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Supramolecule #1: Type III-B Cmr-beta binary complex, crRNA-bound

SupramoleculeName: Type III-B Cmr-beta binary complex, crRNA-bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / Details: Cmr7 part of the complex
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightExperimental: 900 KDa

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Macromolecule #1: CRISPR-associated protein, Cmr5 family

MacromoleculeName: CRISPR-associated protein, Cmr5 family / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus (strain REY15A) (acidophilic)
Molecular weightTheoretical: 17.961834 KDa
SequenceString:
MLYEEDYKLA LEAFKKVFNA LTHYGAKQAF RSRARDLVEE IYNSGFIPTF FYIISKAELN SDSLDSLISL FSSDNAILRG SDENVSYSA YLFIILYYLI KRGIIEQKFL IQALRCEKTR LDLIDKLYNL APIISAKIRT YLLAIKRLSE ALIEAR

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Macromolecule #2: CRISPR-associated RAMP protein, Cmr4 family

MacromoleculeName: CRISPR-associated RAMP protein, Cmr4 family / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus (strain REY15A) (acidophilic)
Molecular weightTheoretical: 32.366371 KDa
SequenceString: MPYYAFAEPF FIHAITHLHV GSGSSVEEEI DLPFQRDELG YPTIYASSLK GAIKSFLLKE FPDKRDVIYK VLGEDENPEE ASLGTFLDA ILFAIPSRII EIDSAKPYVW VYVTTYELLK KVKLYLDSIS QLSNASFSNL KNKIDTILAK EGKNITLDSD L KSAILNED ...String:
MPYYAFAEPF FIHAITHLHV GSGSSVEEEI DLPFQRDELG YPTIYASSLK GAIKSFLLKE FPDKRDVIYK VLGEDENPEE ASLGTFLDA ILFAIPSRII EIDSAKPYVW VYVTTYELLK KVKLYLDSIS QLSNASFSNL KNKIDTILAK EGKNITLDSD L KSAILNED FYVELEALNN KIPSIINAGV PLLVLEDSIG REVINRSLIR VRRIRIDRDK KVVETGGLWS EEYVPMKTIF FS VLLGKES KESAIFASCI LRNLRYVILG GKETIGKGIV ELRWVKDVI

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Macromolecule #3: CRISPR-associated protein, Cmr3 family

MacromoleculeName: CRISPR-associated protein, Cmr3 family / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus (strain REY15A) (acidophilic)
Molecular weightTheoretical: 36.008547 KDa
SequenceString: MKRVLIKPLE PLMFRSQGEF EPLITGSHTA AQSLIIPRPS TIAGMLGYIL FNKSSGTGDW LSDLTNLLAT IYGTFIETNG EYLFPLRMG NHLALVDQQH LINLPTLLEK EYERREKGIY ELFYDKNKLF QIINHQDRIG ISIDKSTRTV KEHYLYSARY L AFKKEVNY ...String:
MKRVLIKPLE PLMFRSQGEF EPLITGSHTA AQSLIIPRPS TIAGMLGYIL FNKSSGTGDW LSDLTNLLAT IYGTFIETNG EYLFPLRMG NHLALVDQQH LINLPTLLEK EYERREKGIY ELFYDKNKLF QIINHQDRIG ISIDKSTRTV KEHYLYSARY L AFKKEVNY VIFIDNDAIS DKINGKIVNF GGENRIAKLE VDDYKVDTSI EEEYYLALSP ILIPDEALDN FLDNISDYVA MG KVDKISL GFDIANTKRK EMLTAILEGS IVKRSIIDFI KNEIKNDLRY RFSKYEKIGY NTLMSLCKLA LRKILS

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Macromolecule #4: CRISPR-associated RAMP protein, Cmr6 family

MacromoleculeName: CRISPR-associated RAMP protein, Cmr6 family / type: protein_or_peptide / ID: 4 / Details: C-terminally histidine-tagged / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus (strain REY15A) (acidophilic)
Strain: REY15A
Molecular weightTheoretical: 33.945914 KDa
Recombinant expressionOrganism: Sulfolobus islandicus (strain REY15A) (acidophilic)
SequenceString: MAIDFLVNIL ELIKEKQCNI NLFSAISLTS IVYNNFGEFL SNNQSYSTNN PLLKYHIIIL NDKNKTKDVE EKRNIFKREV AELISRNFK LDGEKVRNYF DSLKEVLKSL KYTIVDVEIT TRTRALIGVS TSLGKLIFGS GISFDPYMNL PYIPASEIKG I VRSYIEGK ...String:
MAIDFLVNIL ELIKEKQCNI NLFSAISLTS IVYNNFGEFL SNNQSYSTNN PLLKYHIIIL NDKNKTKDVE EKRNIFKREV AELISRNFK LDGEKVRNYF DSLKEVLKSL KYTIVDVEIT TRTRALIGVS TSLGKLIFGS GISFDPYMNL PYIPASEIKG I VRSYIEGK LGEQEAEEIF GNEEREGNVN FTDAYPTRSK DFLFVPDVIT PHYNGKKSEA DAEPRPVIHL TIAPKVTFRF LI YYKREDV GKPICDSMPI ILIRGLGARS SVGYSLFELR KIEVIKAAAH HHHHHHHHH

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Macromolecule #5: Cmr1

MacromoleculeName: Cmr1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 55.388965 KDa
SequenceString: MEELLMSLKL KALYPLTGGY NRHSINPFYE ELVRPTEIKG LWRWWNRVLF NTLAYSTKGK LYTYESIDRL FEDVFGSENK KSAVRLEVI TDEGNDNRFE LSYVELDKVI DCLRNYKRKV SLDFIDNTLI AEIEGSTKIP ISFKSNLDID KIIKDLVHNN K LLSFELLG ...String:
MEELLMSLKL KALYPLTGGY NRHSINPFYE ELVRPTEIKG LWRWWNRVLF NTLAYSTKGK LYTYESIDRL FEDVFGSENK KSAVRLEVI TDEGNDNRFE LSYVELDKVI DCLRNYKRKV SLDFIDNTLI AEIEGSTKIP ISFKSNLDID KIIKDLVHNN K LLSFELLG FKSVEIDATK ISDKKILKEI LRDLITNYLE YFNIKQEVTF TLNIYLDKSR EHKQNFEDKL KFALYSLLVF IL LGGIGRK TSRGFGSLSI IDVKCYDNSI CKKIEDLAKN FLKISSGNEL KSKIESILDC IKNSCIDTLY IENNILSEID PKK NVVYFI NSDLFEVKRI NDKEKVLANI YKAVSSEGCC IKSIITDKYV RKSFLIAFGG YRKVEKDKGL DIGFIKNYLC ETCE TVSSF NIVDFLLSEG SFMSDYILQY EHRNSLLRFK LISDNSNNSY LIGYILHSSY FKKIDIKYVR CILEKLTYCV I

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Macromolecule #6: CRISPR-associated protein, Cmr2 family

MacromoleculeName: CRISPR-associated protein, Cmr2 family / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus (strain REY15A) (acidophilic)
Molecular weightTheoretical: 120.856453 KDa
SequenceString: MSIDNVLREF LDYKIIALLH DPPNKAWVIT GRARNLTQQL SNIRASRKHE KVAKYIINQL FGKNYSEKVD NADKLASSID RYLGSIVYK ERSLFENRSI FLKNILLSNI QRDIGNLFPK DKSKLDNLIL EYKKLLNVIN KTNLILKYQL FYLIYELVWI D SKYENTPS ...String:
MSIDNVLREF LDYKIIALLH DPPNKAWVIT GRARNLTQQL SNIRASRKHE KVAKYIINQL FGKNYSEKVD NADKLASSID RYLGSIVYK ERSLFENRSI FLKNILLSNI QRDIGNLFPK DKSKLDNLIL EYKKLLNVIN KTNLILKYQL FYLIYELVWI D SKYENTPS DTRNPTHTIF DHLYATAAMM NWILSLEKEA KGYLLGIDTI GVADFISKGR KTRDLWISSY LVSALLWYVI TW FIEEYGP DVILFPSLRF NQFYAFYLLE KLRKEGVSED VIDEIKELIT KYIFNGDDLF ENLKIPPYPI IPGRITLILP GLI REGEEY KKVQDDNCFI SKVKERYNEG WRKLIEGLRC YSERKREDGF WNLVCRVLKL TEDLLQTTPL NIRVKQVSVT EDEI FNNNK LRSDSWKIYD NKYRQLVSEF KKSKLVKVTP ESRLKLFELT KFDKLPQIGE KSKRGYEFCT SCGVLPAVVI MPKED ELEK KLIDLGIARD EKDVRSIKNM ISPGERLCPW CLVKRALGAE PRLMRILLLG DLYSVEKIVN EIVSRDVKIE IPSTSD IAS IKTFEEMIEK KNEICEDLKE EEVCEKPSES VLSMWQWFNK NYYNGINLTI DPEEYWFSEK RRRYYFSVFR RHRITFP SP YYALVRADSD YLGDLLEGKL TPYLAGIIDS GDYANISEKK EEVNKLLEEY LVNAGSGSIV DYVKTVLKCI RENLNKCS C AEKIYSNEVA KVMFRVNVEK ANVEEEVKNS LEYFETILNE GRIIVTPAWH VSISSALNRG LLVELELVNK HKGFVIYAG GDDLLAMLPV DEVLDFIKES RRAFAGFGTE KLGNMCLENG FVRINNAYYP SLPIVGRSYS VIIAHYADPL FFVINDSYNL LEEGKEIIR YRVMYNGEYK DAKKDVAIFR YQGLTSVIPL SLKRPIVSSV SDFNEIASII DVILELKKRI DEGRISVSLL Y DYEKYKHL IVASDEKYLT EFLVKDWIKR NSLRKHVEFT IDEKLYGVRL TIENYPIKIP NDLISNIVYT LRIIYGGEK

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Macromolecule #8: CRISPR-associated protein Cmrx

MacromoleculeName: CRISPR-associated protein Cmrx / type: protein_or_peptide / ID: 8 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus islandicus (strain REY15A) (acidophilic)
Molecular weightTheoretical: 19.705607 KDa
SequenceString:
MSTQREYVFI PITNSITIDV KITIGGSDHI TNIDERGIHN VLVITGYAVD EKNGRLVPTL DPCDYVKGIL VAGTPQQAQS NDFLTLKLP ANKLYLIRKK GNISDDLKIY IPYSSPDARN SMKTKPVSIS DDTIVNNIIK EVFDKIYNIT QKEKVKIEKV K EDIKELFS YYALEQ

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Macromolecule #7: crRNA (51-mer)

MacromoleculeName: crRNA (51-mer) / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Molecular weightTheoretical: 16.409871 KDa
SequenceString:
AUUGAAAGUU CAAAGCUUAG AUACCCUGGA GGGAAACCAG ACUUAACACC A

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.15 MNaClsodium chloride
0.01 MTris-HCl
GridModel: Quantifoil, UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Leica EM ACE200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3-4 s blotting before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2792 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 614000
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER
Details: Model generated ab initio with cisTEM using a dataset of a similar sample.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Software - details: beta / Number images used: 69043
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Software - details: beta
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0) / Software - details: beta
Final 3D classificationNumber classes: 3 / Avg.num./class: 32000 / Software - Name: cisTEM (ver. 1.0) / Software - details: beta
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-6s6b:
Type III-B Cmr-beta Cryo-EM structure of the Apo state

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